Transcription
1. What is transcription?
The process by which a DNA sequence produces an RNA molecule. It is the primary control of gene expression.
2. What are transcription factor/s?
They are the proteins helping the process of transcription. These proteins initiate and regulate the process of transcription.
3. What is the distinctive feature of transcription factor/s?
They have a DNA-binding domain that enables them to bind with specific sequences of DNA called enhancers or promoter sequences.
Some transcription factors bind to a DNA promoter sequence near the site of transcription and help form the transcription initiation complex. On the other hand, other transcription factors bind to regulatory sequences, such as enhancers sequences, and can either stimulate or repress transcription of related genes. These regulatory sequences can be thousands of base pairs upstream and downstream from the gene being transcribed. Regulation of genes helps in gene control. Thus, these transcription factors allow expression of each gene in different cell types and during development.
The steps of transcription are initiation, elongation and termination.
TATA BOX
1. What is a TATA box?
It is a DNA sequence that indicates the region from which genetic sequence is read and decoded. It is a type of promoter sequence specifying other molecules to initiate the process of transcription. It is named because of a conserved sequence most commonly called TATAAA. It can also be called a promoter sequence.
2. Where is the TATA box located in eukaryotic genes?
It is located 25-35 base pairs before the transcription site of a gene starts.
3. What is the importance of the TATA box?
The TATA box helps in defining the direction of transcription and also indicates the DNA strand to be read. It further provides binding of transcription factor (proteins) and recruits an enzyme called RNA polymerase which synthesizes RNA from DNA.
Poly A tail
1. What is poly A tail?
It is a long chain of adenine nucleotides that is added to a messenger (mRNA) in course of RNA processing.
2. Why does polyadenylation occur?
The process of addition of adenine nucleotides at 3’ end of the transcript is called polyadenylation. It occurs for following reasons:
i) It makes the RNA molecule more stable and prevents its degradation.
ii) It allows mature RNA molecules to be exported from nucleus to cytoplasm where protein synthesis occurs by the help of ribosomes.
3. What is RNA processing?
It refers to modification of newly synthesized RNA occurring immediately after a gene in an eukaryotic cell is transcribed. Modification occurs in both ends of the primary transcript to produce a mature mRNA.
4. How does adenylation occur?
The process starts with the cleavage of 3’ end of primary transcript which is cleaved to a free 3’ hydroxyl end. Then, an enzyme called poly-A polymerase adds a chain of adenine nucleotides to the RNA. The poly-A tail so added is between 100 and 250 residues long.
RNA polymerase
There are three types of RNA polymerase found in eukaryotes while only one in case prokaryotes.
Replisome
The manner or organized assembly by which proteins are engaged in DNA replication at the replication fork is called replisome.
Replicon
The replicative unit consisting either part or whole of the genome is considered a replicon. For instance, in Escherichia coli, the entire genome contributes as a replicon.
AAA + protein
ATPase associated with various activities, which are mostly involved in the assembly of the replisome.
Primase
Enzyme that synthesizes an RNA primer for DNA replication.
Replication
Act of making a copy of the genome of the cell.
Topoisomerase
The enzyme that alters the topology of DNA. They are of two types i.e. Type I topoisomerase and type II topoisomerase. Type I topoisomerase acts on one strand at a time while type II acts on two strands at a time. Gyrase and topoisomerase IV are type II enzymes. The subunits of gyrase are encoded by gyrA and gyrB gene while that of topoisomerase IV are encoded by parC and parE genes.
DNA gyrase introduces negative supercoils into DNA that requires ATP hydrolysis mediated by gyrB subunit. In prokaryotes, gyrase and topoisomerase IV are composed of two subunits A and B which associate to form A2B2 complex in active enzyme.
In human and yeast type II topoisomerase are large single-subunit enzymes that are active as homodimers.
Helicase
Enzyme that unwinds DNA and requires adenosine triphosphate (ATP).
Ligase
Enzyme that joins strands of DNA covalently.
Polymerase
Enzyme that synthesizes a nucleic acid.
Steps in DNA replication
There are three steps in DNA replication. They are initiation, elongation and termination.
Origin Replication complex (ORC) / OriC
The origin replication complex (ORC) is a six-subunit that acts as the initiator at eukaryotic origins of replication.
Clamp Loaders
They are pentameric ATPases of the AAA+ family which helps in operating to ensure processive DNA replication. In between the five subunits arranged in a circle, there is a gap between the first and the fifth subunits (because of missing sixth units). They are designated from A to E starting with the subunit at the open interface and proceeding counter-clockwise around the clamp loader. Each subunit has three domains. The amino-acid terminal domain and its adjacent domain assume the fold of AAA+ proteins and the subunits are held together in a ring by carboxy-terminal domains forming a tight pentameric collar together.
Nucleic acids
Nucleic acids are long polynucleotide chains formed by phosphodiester bonds between the 5′-phosphate of one nucleotide and the 3′-hydroxyl (OH) of the adjacent nucleotide.
Nucleotide
Nucleotides are the building blocks of DNA and RNA. They are composed of a base, typically A, G, C, T in DNA and A, G, C, U in RNA, that is joined by a N-glycosidic linkage to a sugar, deoxyribose in DNA, or ribose in RNA; one or more phosphate groups are attached to the sugar, typically at the 5′ or 3′ position.
Phosphodiester bond
Phosphodiester bonds join one nucleotide to the next nucleotide to form long polynucleotide chains.
RNase
A nuclease that degrades single-or double-stranded RNA.
DNase
A nuclease that degrades single-or double-stranded DNA.
Endonuclease
A nuclease that cleaves the phosphodiester backbone of nucleic acids at internal sites in the polynucleotide chain of single-or double-stranded nucleic acid.
Exonuclease
A nuclease that degrades nucleic acids one nucleotide at a time by sequential cleavages of the phosphodiester backbone from either the 5′-or 3′-end. 5′→3′ exonucleases degrade from the 5′-end of the polynucleotide chain and 3′→5′ exonucleases degrade from the 3′-end. They can work on single-or double-stranded nucleic acids.
DNA polymerase proofreading
Many DNA polymerases that are responsible for chromosome replication have a 3′→5′ exonuclease activity that resides in the same protein as the polymerase activity or in a closely interacting subunit. The 3′→5′ exonuclease activity preferentially removes incorrect nucleotides from the primer end and, thus, acts as a proofreader for the DNA polymerase. DNA polymerase exonucleolytic proofreading can increase the fidelity of DNA replication by 100-fold.
DNA repair
A process in which a region of damaged DNA is cut out by nucleases. While some types of DNA repair do not require cutting DNA, nucleases perform critical steps in most DNA repair pathways.
Recognition sequence (recognition site)
A DNA sequence that is recognized by both the methyltransferase and the endonuclease of a restriction–modification system; usually a unique (but sometimes a degenerate) sequence of nucleotides 4 – 8 bp long, though many are interrupted by a DNA segment of unspecified sequence but specified length.
Restriction enzyme (or endonuclease)
The endonuclease component of a restriction–modification system. These enzymes cleave DNA with unmodified recognition sites, in some (but not all) instances at fixed locations relative to the recognition sequence.
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